Abstract: Diatoms are one of the major primary producers supporting food webs in the ocean. Their
productivity could be linked to community composition. Temporal and spatial variation of
diatom communities may correlate with nitrogen sources and availability. In order to understand
the changes in diatom communities related to environmental variations, molecular tools targeting
nitrate transporter genes in diatoms were developed and applied to examine diatom communities
in Onslow Bay, North Carolina, and Monterey Bay, California. Cloning, sequencing and
Distance-Based OTU and Richness (DOTUR) analyses were used to investigate patterns of
diversity over time and space. Terminal Restriction Fragment Length Polymorphism (T-RFLP),
Cannonical Correspondence Analysis (CCA) and simple linear regression analyses were
conducted to compare community dynamics to variations in environmental parameters. In
Onslow Bay, the composition of diatom communities was highly varied in different seasons and
locations. Temperature differences appeared to influence the changes in diatom communities
more than dissolved inorganic nitrogen. In Monterey Bay, temporal variation was higher in
diatom communities as compared to depth profiles. Changes in temperature, silica, and nitrate
appeared to influence the composition of diatom assemblages. This study demonstrated the
potential usage of molecular tools to monitor diatom communities and to determine the
environmental factors affecting the composition of diatom assemblages in nature. This will help
to gain a better understanding of phytoplankton community dynamics in the oceans.